From Methylome to Integrative Analysis of Tissue Specificity

Thomas Dugé de Bernonville; Christian Daviaud; Cristian Chaparro; Jörg Tost; Stéphane Maury

doi:10.1007/978-1-0716-2349-7_16

From Methylome to Integrative Analysis of Tissue Specificity

Methods Mol Biol. 2022:2505:223-240. doi: 10.1007/978-1-0716-2349-7_16.

Authors

Thomas Dugé de Bernonville^#^{1

2}, Christian Daviaud^#³, Cristian Chaparro⁴, Jörg Tost³, Stéphane Maury⁵

Affiliations

¹ EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France.
² Limagrain, Centre de Recherches de Chappes, Route d'Ennezat, Chappes, France.
³ Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris Saclay, Evry, France.
⁴ UMR5244 IHPE, Université Montpellier, CNRS, IFREMER, Université Perpignan, Perpignan, France.
⁵ EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAe, Université d'Orléans, Orléans, France. [email protected].

^# Contributed equally.

PMID: 35732948
DOI: 10.1007/978-1-0716-2349-7_16

Abstract

DNA methylation is the most studied epigenetic mark in both plants and animals. The gold standard for assaying genome-wide DNA methylation at single-base resolution is whole-genome bisulfite sequencing (WGBS). Here, we describe an improved procedure for WGBS and original bioinformatic workflows applied to unravel tissue-specific variations of the methylome in relation to gene expression and accumulation of secondary metabolites in the medicinal plant Catharanthus roseus.

Keywords: Catharanthus roseus; DNA methylation; Methylome pipeline; Ovation Methyl-seq; Whole-Genome Bisulfite Sequencing (WGBS).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
DNA / genetics
DNA Methylation
Epigenome*
Epigenomics / methods
High-Throughput Nucleotide Sequencing* / methods
Organ Specificity / genetics
Sequence Analysis, DNA / methods
Sulfites

Substances

Sulfites
DNA